Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009107.1 Kokia drynarioides strain JFW-HI SEQ_123808, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 25652
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:10651 original size:17 final size:18

Alignment explanation


    Indices: 10617--10651  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10607 ATTTTAATGT

                               
      10617 TTATAAAATTGAAATTTTA
          1 TTATAAAATT-AAATTTTA

                             
      10636 TTATAAAATT-AATTTT
          1 TTATAAAATTAAATTTT

      10652 TTTAGTTGCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    6  0.38
  19   10  0.62

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (18 bp):   
TTATAAAATTAAATTTTA

Found at i:11097 original size:19 final size:17

Alignment explanation


    Indices: 11045--11104  Score: 59
    Period size: 17  Copynumber: 3.4  Consensus size: 17

      11035 TATATTAAAA

                *       *    
      11045 TTTATATATTTTATAAT
          1 TTTAAATATTTTTTAAT

                 *           
      11062 TTTAATTA-TTTTTAAT
          1 TTTAAATATTTTTTAAT

                                
      11078 TATTAAATATTTTTTGAATT
          1 T-TTAAATATTTTTT-AA-T

                   
      11098 TTTAAAT
          1 TTTAAAT

      11105 TTTAAAAATA


Statistics
Matches: 35,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
  16    8  0.23
  17   12  0.34
  18    5  0.14
  19    8  0.23
  20    2  0.06

ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63


Consensus pattern (17 bp):   
TTTAAATATTTTTTAAT

Found at i:22128 original size:33 final size:33

Alignment explanation


    Indices: 22091--22156  Score: 80
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      22081 TTAAGTATTT

                                        *     
      22091 ATAATCACTT-CAAATATATCGTGTTGAGTTGTG
          1 ATAATCA-TTACAAATATATCGTGTTGAATTGTG

                 *    *      *               
      22124 ATAATTATTATAAATATGTCGTGTTGAATTGTG
          1 ATAATCATTACAAATATATCGTGTTGAATTGTG

      22157 GCAAAGTCAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  32    2  0.07
  33   26  0.93

ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42


Consensus pattern (33 bp):   
ATAATCATTACAAATATATCGTGTTGAATTGTG

Found at i:23604 original size:59 final size:59

Alignment explanation


    Indices: 23511--23626  Score: 155
    Period size: 59  Copynumber: 2.0  Consensus size: 59

      23501 TCCAATTATT

                                     *           *        *            
      23511 AGTAAATTTTTTATTGGTCAACCAATTATGAAAAAGTTACAAAATGGTCACTCAATTAA
          1 AGTAAATTTTTTATTGGTCAACCAACTATGAAAAAGTCACAAAATGATCACTCAATTAA

                                  * *                                  
      23570 AGTAAATTTCTTT-TATGGTCATCTAACTAT-AAAAAGTCACAAAATGATCACTCAATT
          1 AGTAAATTT-TTTAT-TGGTCAACCAACTATGAAAAAGTCACAAAATGATCACTCAATT

      23627 TCATTCTTGT


Statistics
Matches: 50,  Mismatches: 5, Indels: 4
        0.85            0.08        0.07

Matches are distributed among these distances:
  59   35  0.70
  60   15  0.30

ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34


Consensus pattern (59 bp):   
AGTAAATTTTTTATTGGTCAACCAACTATGAAAAAGTCACAAAATGATCACTCAATTAA

Found at i:24230 original size:23 final size:23

Alignment explanation


    Indices: 24192--24235  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      24182 ATGCACGTAT

                            *      
      24192 TATTTTTAAAATTTTAGTTTTTC
          1 TATTTTTAAAATTTTAATTTTTC

                                  
      24215 TATTTTT-AAATATTTAATTTT
          1 TATTTTTAAAAT-TTTAATTTT

      24236 AGATTTTAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    4  0.21
  23   15  0.79

ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66


Consensus pattern (23 bp):   
TATTTTTAAAATTTTAATTTTTC

Found at i:24994 original size:20 final size:20

Alignment explanation


    Indices: 24971--25010  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      24961 TTTTTAAAAT

                                 
      24971 AATTCTTATT-ATTTTTTTAA
          1 AATT-TTATTGATTTTTTTAA

                  *             
      24991 AATTTTGTTGATTTTTTTAA
          1 AATTTTATTGATTTTTTTAA

      25011 TTCTAAAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    4  0.22
  20   14  0.78

ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65


Consensus pattern (20 bp):   
AATTTTATTGATTTTTTTAA

Found at i:25619 original size:2 final size:2

Alignment explanation


    Indices: 25612--25652  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      25602 ATTCACAATC

                                                                         
      25612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.